4DYD

Substrate-directed dual catalysis of dicarbonyl compounds by diketoreductase

Structural Biology Knowledgebase: 4DYD SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.242
  • R-Value Work: 0.217

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4DYD

Classification: OXIDOREDUCTASE

Total Structure Weight: 32136.87

Macromolecule Entities
Molecule Chains Length Organism Details
Diketoreductase A 283 Acinetobacter baylyi Gene Name(s): dkr
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NAD
Query on NAD

A NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

A PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.242
  • R-Value Work: 0.217
  • Space Group: P 62 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 100.48 α = 90.00
b = 100.48 β = 90.00
c = 131.91 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-02-28
  • Released Date: 2012-11-14
  • Deposition author(s): Lu, M., White, M.A., Huang, Y., Wu, X., Liu, N., Cheng, X., Chen, Y.

Revision History

No revisions since initial release